메뉴 건너뛰기




Volumn 2015, Issue 4, 2015, Pages

Widespread mitovirus sequences in plant genomes

Author keywords

Mycovirus; Narnavirus; NERVE; Plant mitochondria; RNA virus

Indexed keywords

RNA DIRECTED RNA POLYMERASE;

EID: 84926490232     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.876     Document Type: Article
Times cited : (63)

References (49)
  • 1
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: selection of best-fit models of protein evolution
    • Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105 DOI 10.1093/bioinformatics/bti263.
    • (2005) Bioinformatics , vol.21 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 2
    • 79952247426 scopus 로고    scopus 로고
    • Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses
    • Al Rwahnih M, Daubert S, Urbez-Torres JR, Cordero F, Rowhani A. 2011. Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Archives of Virology 156:397-403 DOI 10.1007/s00705-010-0869-8.
    • (2011) Archives of Virology , vol.156 , pp. 397-403
    • Al Rwahnih, M.1    Daubert, S.2    Urbez-Torres, J.R.3    Cordero, F.4    Rowhani, A.5
  • 5
    • 33745256005 scopus 로고    scopus 로고
    • Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative
    • Anisimova M, Gascuel O. 2006. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Systematic Biology 55:539-552 DOI 10.1080/10635150600755453.
    • (2006) Systematic Biology , vol.55 , pp. 539-552
    • Anisimova, M.1    Gascuel, O.2
  • 6
    • 84884518363 scopus 로고    scopus 로고
    • Selectively maintained paleoviruses in Holarctic water fleas reveal an ancient origin for phleboviruses
    • Ballinger MJ, Bruenn JA, Kotov AA, Taylor DJ. 2013. Selectively maintained paleoviruses in Holarctic water fleas reveal an ancient origin for phleboviruses. Virology 446:276-282 DOI 10.1016/j.virol.2013.07.032.
    • (2013) Virology , vol.446 , pp. 276-282
    • Ballinger, M.J.1    Bruenn, J.A.2    Kotov, A.A.3    Taylor, D.J.4
  • 7
    • 84864566166 scopus 로고    scopus 로고
    • Phylogeny, integration and expression of sigma virus-like genes in Drosophila
    • Ballinger MJ, Bruenn JA, Taylor DJ. 2012. Phylogeny, integration and expression of sigma virus-like genes in Drosophila. Molecular Phylogenetics and Evolution 65:251-258 DOI 10.1016/j.ympev.2012.06.008.
    • (2012) Molecular Phylogenetics and Evolution , vol.65 , pp. 251-258
    • Ballinger, M.J.1    Bruenn, J.A.2    Taylor, D.J.3
  • 8
    • 84874957024 scopus 로고    scopus 로고
    • Multiplexed interactions: viruses of endophytic fungi
    • Bao X, Roossinck MJ. 2013. Multiplexed interactions: viruses of endophytic fungi. Advances in Virus Research 86:37-58 DOI 10.1016/B978-0-12-394315-6.00002-7.
    • (2013) Advances in Virus Research , vol.86 , pp. 37-58
    • Bao, X.1    Roossinck, M.J.2
  • 9
    • 0037386414 scopus 로고    scopus 로고
    • A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases
    • Bruenn JA. 2003. A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases. Nucleic Acids Research 31:1821-1829 DOI 10.1093/nar/gkg277.
    • (2003) Nucleic Acids Research , vol.31 , pp. 1821-1829
    • Bruenn, J.A.1
  • 10
    • 84855322610 scopus 로고    scopus 로고
    • A member of the virus family Narnaviridae from the plant pathogenic oomycete Phytophthora infestans
    • Cai G, Myers K, Fry WE, Hillman BI. 2012. A member of the virus family Narnaviridae from the plant pathogenic oomycete Phytophthora infestans. Archives of Virology 157:165-169 DOI 10.1007/s00705-011-1126-5.
    • (2012) Archives of Virology , vol.157 , pp. 165-169
    • Cai, G.1    Myers, K.2    Fry, W.E.3    Hillman, B.I.4
  • 11
    • 84901423577 scopus 로고    scopus 로고
    • TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction
    • Chang JM, Di Tommaso P, Notredame C. 2014. TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Molecular Biology and Evolution 31:1625-1637 DOI 10.1093/molbev/msu117.
    • (2014) Molecular Biology and Evolution , vol.31 , pp. 1625-1637
    • Chang, J.M.1    Di Tommaso, P.2    Notredame, C.3
  • 14
    • 84858748842 scopus 로고    scopus 로고
    • Endogenous RNA viruses of plants in insect genomes
    • Cui J, Holmes EC. 2012. Endogenous RNA viruses of plants in insect genomes. Virology 427:77-79 DOI 10.1016/j.virol.2012.02.014.
    • (2012) Virology , vol.427 , pp. 77-79
    • Cui, J.1    Holmes, E.C.2
  • 15
    • 84894094543 scopus 로고    scopus 로고
    • Plastid phylogenomics and green plant phylogeny: almost full circle but not quite there
    • Davis CC, Xi Z, Mathews S. 2014. Plastid phylogenomics and green plant phylogeny: almost full circle but not quite there. BMC Biology 12:11 DOI 10.1186/1741-7007-12-11.
    • (2014) BMC Biology , vol.12 , pp. 11
    • Davis, C.C.1    Xi, Z.2    Mathews, S.3
  • 17
    • 0026739803 scopus 로고
    • T double-stranded RNA (dsRNA) sequence reveals that T andWdsRNAs form a new RNA family in Saccharomyces cerevisiae Identification of 23 S RNA as the single-stranded form of T dsRNA
    • Esteban LM, Rodriguez-Cousino N, Esteban R. 1992. T double-stranded RNA (dsRNA) sequence reveals that T andWdsRNAs form a new RNA family in Saccharomyces cerevisiae. Identification of 23 S RNA as the single-stranded form of T dsRNA. Journal of Biological Chemistry 267:10874-10881.
    • (1992) Journal of Biological Chemistry , vol.267 , pp. 10874-10881
    • Esteban, L.M.1    Rodriguez-Cousino, N.2    Esteban, R.3
  • 19
    • 0031033796 scopus 로고    scopus 로고
    • RNA-dependent RNA polymerase activity associated with the yeast viral p91/20S RNA ribonucleoprotein complex
    • Garcia-Cuellar MP, Esteban R, Fujimura T. 1997. RNA-dependent RNA polymerase activity associated with the yeast viral p91/20S RNA ribonucleoprotein complex. RNA 3:27-36.
    • (1997) RNA , vol.3 , pp. 27-36
    • Garcia-Cuellar, M.P.1    Esteban, R.2    Fujimura, T.3
  • 21
    • 0033983852 scopus 로고    scopus 로고
    • Phylogenetic analysis of some large double-stranded RNA replicons from plants suggests they evolved from a defective single-stranded RNA virus
    • Gibbs MJ, Koga R, Moriyama H, Pfeiffer P, Fukuhara T. 2000. Phylogenetic analysis of some large double-stranded RNA replicons from plants suggests they evolved from a defective single-stranded RNA virus. Journal of General Virology 81:227-233.
    • (2000) Journal of General Virology , vol.81 , pp. 227-233
    • Gibbs, M.J.1    Koga, R.2    Moriyama, H.3    Pfeiffer, P.4    Fukuhara, T.5
  • 22
    • 84874957438 scopus 로고    scopus 로고
    • The family narnaviridae: simplest of RNA viruses
    • Hillman BI, Cai G. 2013. The family narnaviridae: simplest of RNA viruses. Advances in Virus Research 86:149-176 DOI 10.1016/B978-0-12-394315-6.00006-4.
    • (2013) Advances in Virus Research , vol.86 , pp. 149-176
    • Hillman, B.I.1    Cai, G.2
  • 23
    • 0032551233 scopus 로고    scopus 로고
    • Evolutionary relationships among putative RNA-dependent RNA polymerases encoded by a mitochondrial virus-like RNA in the Dutch elm disease fungus, Ophiostoma novo-ulmi, by other viruses and virus-like RNAs and by the Arabidopsis mitochondrial genome
    • Hong Y, Cole TE, Brasier CM, Buck KW. 1998. Evolutionary relationships among putative RNA-dependent RNA polymerases encoded by a mitochondrial virus-like RNA in the Dutch elm disease fungus, Ophiostoma novo-ulmi, by other viruses and virus-like RNAs and by the Arabidopsis mitochondrial genome. Virology 246:158-169 DOI 10.1006/viro.1998.9178.
    • (1998) Virology , vol.246 , pp. 158-169
    • Hong, Y.1    Cole, T.E.2    Brasier, C.M.3    Buck, K.W.4
  • 25
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30:3059-3066 DOI 10.1093/nar/gkf436.
    • (2002) Nucleic Acids Research , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 26
    • 78649718268 scopus 로고    scopus 로고
    • Endogenous viral elements in animal genomes
    • Katzourakis A, Gifford RJ. 2010. Endogenous viral elements in animal genomes. PLoS Genetics 6:e1001191 DOI 10.1371/journal.pgen.1001191.
    • (2010) PLoS Genetics , vol.6
    • Katzourakis, A.1    Gifford, R.J.2
  • 29
    • 84885949870 scopus 로고    scopus 로고
    • A virocentric perspective on the evolution of life
    • Koonin EV, Dolja VV. 2013. A virocentric perspective on the evolution of life. Current Opinion in Virology 3:546-557 DOI 10.1016/j.coviro.2013.06.008.
    • (2013) Current Opinion in Virology , vol.3 , pp. 546-557
    • Koonin, E.V.1    Dolja, V.V.2
  • 30
    • 84886801257 scopus 로고    scopus 로고
    • Virus world as an evolutionary network of viruses and capsidless selfish elements
    • Koonin EV, Dolja VV. 2014. Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiology and Molecular Biology Reviews 78:278-303 DOI 10.1128/MMBR.00049-13.
    • (2014) Microbiology and Molecular Biology Reviews , vol.78 , pp. 278-303
    • Koonin, E.V.1    Dolja, V.V.2
  • 31
    • 80054780694 scopus 로고    scopus 로고
    • Role of intercompartmental DNA transfer in producing genetic diversity
    • Leister D, Kleine T. 2011. Role of intercompartmental DNA transfer in producing genetic diversity. International Review of Cell and Molecular Biology 291:73-114 DOI 10.1016/B978-0-12-386035-4.00003-3.
    • (2011) International Review of Cell and Molecular Biology , vol.291 , pp. 73-114
    • Leister, D.1    Kleine, T.2
  • 32
    • 38949151064 scopus 로고    scopus 로고
    • How to usefully compare homologous plant genes and chromosomes as DNA sequences
    • Lyons E, Freeling M. 2008. How to usefully compare homologous plant genes and chromosomes as DNA sequences. The Plant Journal 53:661-673 DOI 10.1111/j.1365-313X.2007.03326.x.
    • (2008) The Plant Journal , vol.53 , pp. 661-673
    • Lyons, E.1    Freeling, M.2
  • 33
    • 0031183347 scopus 로고    scopus 로고
    • Viral nucleic acid sequence transfer between fungi and plants
    • Marienfeld JR, Unseld M, Brandt P, Brennicke A. 1997. Viral nucleic acid sequence transfer between fungi and plants. Trends in Genetics 13:260-261 DOI 10.1016/S0168-9525(97)01168-2.
    • (1997) Trends in Genetics , vol.13 , pp. 260-261
    • Marienfeld, J.R.1    Unseld, M.2    Brandt, P.3    Brennicke, A.4
  • 34
    • 9644279629 scopus 로고    scopus 로고
    • Nucleotide sequence of a mitochondrial RNA virus from the plant pathogenic fungus, Helicobasidium mompa Tanaka
    • Osaki H, Nakamura H, Nomura K, Matsumoto N, Yoshida K. 2005. Nucleotide sequence of a mitochondrial RNA virus from the plant pathogenic fungus, Helicobasidium mompa Tanaka. Virus Research 107:39-46 DOI 10.1016/j.virusres.2004.06.010.
    • (2005) Virus Research , vol.107 , pp. 39-46
    • Osaki, H.1    Nakamura, H.2    Nomura, K.3    Matsumoto, N.4    Yoshida, K.5
  • 35
    • 0024259002 scopus 로고
    • Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence
    • Palmer JD, Herbon LA. 1988. Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. Journal of Molecular Evolution 28:87-97 DOI 10.1007/BF02143500.
    • (1988) Journal of Molecular Evolution , vol.28 , pp. 87-97
    • Palmer, J.D.1    Herbon, L.A.2
  • 36
    • 70350512876 scopus 로고    scopus 로고
    • Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin
    • Rastgou M, Habibi MK, Izadpanah K, Masenga V, Milne RG, Wolf YI, Koonin EV, Turina M. 2009. Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin. Journal of General Virology 90:2525-2535 DOI 10.1099/vir.0.013086-0.
    • (2009) Journal of General Virology , vol.90 , pp. 2525-2535
    • Rastgou, M.1    Habibi, M.K.2    Izadpanah, K.3    Masenga, V.4    Milne, R.G.5    Wolf, Y.I.6    Koonin, E.V.7    Turina, M.8
  • 37
    • 0014945264 scopus 로고
    • A multiple origin for plastids and mitochondria
    • Raven PH. 1970. A multiple origin for plastids and mitochondria. Science 169:641-646 DOI 10.1126/science.169.3946.641.
    • (1970) Science , vol.169 , pp. 641-646
    • Raven, P.H.1
  • 38
    • 0026736438 scopus 로고
    • Both yeast W double-stranded RNA and its single-stranded form 20S RNA are linear
    • Rodriguez-Cousino N, Esteban R. 1992. Both yeast W double-stranded RNA and its single-stranded form 20S RNA are linear. Nucleic Acids Research 20:2761-2766 DOI 10.1093/nar/20.11.2761.
    • (1992) Nucleic Acids Research , vol.20 , pp. 2761-2766
    • Rodriguez-Cousino, N.1    Esteban, R.2
  • 39
    • 0025914520 scopus 로고
    • Molecular cloning and characterization of W double-stranded RNA, a linear molecule present in Saccharomyces cerevisiae Identification of its single-stranded RNA form as 20 S RNA
    • Rodriguez-Cousino N, Esteban LM, Esteban R. 1991. Molecular cloning and characterization of W double-stranded RNA, a linear molecule present in Saccharomyces cerevisiae. Identification of its single-stranded RNA form as 20 S RNA. Journal of Biological Chemistry 266:12772-12778.
    • (1991) Journal of Biological Chemistry , vol.266 , pp. 12772-12778
    • Rodriguez-Cousino, N.1    Esteban, L.M.2    Esteban, R.3
  • 41
    • 49049103327 scopus 로고    scopus 로고
    • The role of alternative genetic codes in viral evolution and emergence
    • Shackelton LA, Holmes EC. 2008. The role of alternative genetic codes in viral evolution and emergence. Journal of Theoretical Biology 254:128-134 DOI 10.1016/j.jtbi.2008.05.024.
    • (2008) Journal of Theoretical Biology , vol.254 , pp. 128-134
    • Shackelton, L.A.1    Holmes, E.C.2
  • 43
    • 84877153523 scopus 로고    scopus 로고
    • Virus-host co-evolution under a modified nuclear genetic code
    • Taylor DJ, Ballinger MJ, Bowman SM, Bruenn JA. 2013. Virus-host co-evolution under a modified nuclear genetic code. PeerJ 1:e50 DOI 10.7717/peerj.50.
    • (2013) PeerJ , vol.1
    • Taylor, D.J.1    Ballinger, M.J.2    Bowman, S.M.3    Bruenn, J.A.4
  • 44
    • 84903786201 scopus 로고    scopus 로고
    • The evolution of novel fungal genes from non-retroviral RNA viruses
    • Taylor DJ, Bruenn J. 2009. The evolution of novel fungal genes from non-retroviral RNA viruses. BMC Biology 7:88 DOI 10.1186/1741-7007-7-88.
    • (2009) BMC Biology , vol.7 , pp. 88
    • Taylor, D.J.1    Bruenn, J.2
  • 46
    • 77953665114 scopus 로고    scopus 로고
    • Filoviruses are ancient and integrated into mammalian genomes
    • Taylor DJ, Leach RW, Bruenn J. 2010. Filoviruses are ancient and integrated into mammalian genomes. BMC Evolutionary Biology 10:193 DOI 10.1186/1471-2148-10-193.
    • (2010) BMC Evolutionary Biology , vol.10 , pp. 193
    • Taylor, D.J.1    Leach, R.W.2    Bruenn, J.3
  • 49
    • 84922796520 scopus 로고    scopus 로고
    • A mitovirus related to plant mitochondrial gene confers hypovirulence on the phytopathogenic fungus Sclerotinia sclerotiorum
    • Xu Z, Wu S, Liu L, Cheng J, Fu Y, Jiang D, Xie J. 2015. A mitovirus related to plant mitochondrial gene confers hypovirulence on the phytopathogenic fungus Sclerotinia sclerotiorum. Virus Research 197:127-136 DOI 10.1016/j.virusres.2014.12.023.
    • (2015) Virus Research , vol.197 , pp. 127-136
    • Xu, Z.1    Wu, S.2    Liu, L.3    Cheng, J.4    Fu, Y.5    Jiang, D.6    Xie, J.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.